Unable to compile "init_atmosphere" core, "undefined reference to `ncmpi_open'"

[Syize]

Compile "init_atmosphere" core failed with following settings:

CORE=init_atmosphere
OPENMP=ture
make gfortran

error messages from make are:

/usr/bin/ld: /home/liurw/Apps/MPAS/src/external/SMIOL/libsmiol.a(smiol.o): in function `SMIOL_open_file':
smiol.c:(.text+0x5bb): undefined reference to `ncmpi_open'
/usr/bin/ld: smiol.c:(.text+0x5ea): undefined reference to `ncmpi_buffer_attach'
/usr/bin/ld: smiol.c:(.text+0x63b): undefined reference to `ncmpi_create'
......

These "ncmpi_*" symbol is from "libpnetcdf.a", which should be linked at the final step.

After checking the log, it seems the compile command:

mpif90 -O3 -L/usr/lib/x86_64-linux-gnu -lpnetcdf -fopenmp -o init_atmosphere_model driver/*.o -L. -ldycore -lops -lframework -L/home/liurw/Apps/MPAS/src/external/SMIOL -lsmiolf -lsmiol -I./external/esmf_time_f90 -L./external/esmf_time_f90 -lesmf_time

should be

mpif90 -O3 -fopenmp -L/usr/lib/x86_64-linux-gnu -o init_atmosphere_model driver/*.o -L. -ldycore -lops -lframework -L/home/liurw/Apps/MPAS/src/external/SMIOL -lsmiolf -lsmiol -I./external/esmf_time_f90 -L./external/esmf_time_f90 -lesmf_time -lpnetcdf

Adding -lpnetcdf to src/Makefile solve this issue.

mpas: $(AUTOCLEAN_DEPS) externals frame ops dycore drver
        $(LINKER) $(LDFLAGS) -o $(EXE_NAME) driver/*.o -L. -ldycore -lops -lframework $(LIBS) -I./external/esmf_time_f90 -L./external/esmf_time_f90 -lesmf_time -lpnetcdf

---

• Compiler and version: gcc & gfortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
• MPI implementation and version: openmpi 4.1.2-2ubuntu1 amd64
• NetCDF version: netcdf 4.8.1-1 amd64
• Parallel NetCDF version: pnetcdf 4.8.1-2 amd64
• Parallel IO version: PIO 2.6.2
• Output of uname -a

  $ uname -a     
  Linux seafogAI 6.5.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May  7 09:00:52 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

• The make line used to build the executable: make gfortran

[mgduda]

Have you set the PNETCDF environment variable to the installation path for Parallel-netCDF?

[Syize]

Thanks for reply. It turns out I forget to set NETCDF, PNETCDF and PIO environment variables when building init_atmosphere core : )